Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

78ddadec-24d0-4d49-b218-f8124bf8634f - samples

ABSTRACT: Microbiome analysis was performed on the patient samples collected pre-FMT and on days after FMT, and on samples collected from the FMT donor. Genomic bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool kit (Qiagen, Hilden, Germany), with the addition of a bead-beating lysis step. Genomic 16S ribosomal-RNA V4 variable regions were amplified and sequenced on the Illumina MiSeq platform.

PROVIDER: EGAD00001004371 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Evaluating the protein extraction methods for gut metaproteomics

Project description:Human stool samples were collected, microbial cells were harvested and subjected to protein extraction using different protocols for metaproteomics analyses. The protein extraction methods differ from the usage of different lysis buffer (SDS, urea and commercially available B-Per reagent), bead beating, ultrasonication and heating. The impacts of different protein extraction methods on metaproteomics results were evaluated with multiple criteria including protein yields, peptide identifications, taxonomic compositions and functional compositions.

2017-07-17 | PXD005969 | Pride

Mouse gut metaproteome - MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

Project description:The mouse stool samples were collected from different diets fed mice and bacterial cells were harvest for metaproteomic analysis for understanding the role ofdiet on gut microbiota.

2016-07-05 | PXD003527 | Pride

gut metagenome

Project description:Bacterial 16S ribosomal RNA genes from stool samples. Targeted Locus (Loci)

| PRJNA276911 | ENA

The Microbiome, Epigenome, and Diet in Adults with Obesity During Behavioral Weight Loss

Project description:Whole blood, stool samples, and questionnaire data were collected from participants in the DRIFT2 trial at baseline and at a 3 month follow-up visit to analyze relationships between DNA methylation, gut microbes, and diet data. 128 total whole blood samples were collected .

2023-08-30 | GSE240184 | GEO

Project description:16S ribosomal RNA sequencing of human stool samples

| PRJNA588869 | ENA

Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics

Project description:A differential lysis approach was developed with different strength of lysis buffers (urea and/or sodium dodecyl sulfate) and applied on human stool samples to separate different microbial species to increase the depth of metaproteomic measurements. We showed that the lysates dominating by proteins from Gram-positive (G+) or negative bacteria (G-) can be achieved by differential lysis

2023-03-27 | PXD016787 | Pride

16S rRNA gene sequence data revealed effects of natural phenylethanoids on gut microbiota.

Project description:The aim of study is to evaluate whether salidroside (S), tyrosol (T) and hydroxytyrosol (H) which are dietary phenylethanoids of natural origins have an influence on reversing gut dysbiosis induced by metabolic syndrome (MetS) mice. C57 BL/6J female mice induced by high fructose diet were established. All mice were adapted to the environment for 7 days with normal diet and sterile drinking water (DW), and randomly divided into 6 groups. Mice in the ND group are fed with ND and treated with normal saline. Other groups were fed with high fructose (HFru) by administration of normal saline, salidroside (S), tyrosol (T) or hydroxytyrosol (H) for 12 weeks by intragastric gavage. Fresh feces from each mouse were collected one days before the end of the experiment and temporarily placed in sterile tubules, and then snap-frozen in liquid nitrogen. Total DNA from stool bacteria was extracted using QIAamp DNA stool mini kit from Qiagen (Germantown, MD, USA) according to the manufacturer’s instructions. Illumina HiSeq sequencing analysis of the DNA samples.16S rRNA gene sequence data further revealed that S, T and H could enhance the diversity of gut microbiota. In general, the abundance of Shigella, Acinetobacter, Lactobacillus, Staphylococcus and Sporosarcina had changed significantly. These findings suggest that S, T and H probably suppress lipid accumulation and to hepatoprotective effect and improve intestinal microflora disorders to attenuate metabolic syndromes.

2022-01-24 | GSE194127 | GEO

Altered fecal small RNA profiles in colorectal cancer reflect gut microbiome composition in stool samples

Project description:Dysbiotic configurations of the human gut microbiota have been linked with colorectal cancer (CRC). Human small non-coding RNAs are also implicated in CRC and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis but their role is less explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens of patients with CRC, or adenomas, and healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We reported a considerable overlap and correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. Furthermore, we identified a combined predictive signature composed by 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC from healthy and adenoma samples (AUC= 0.87). In summary we reported evidence that host-microbiome dysbiosis in CRC can be observed also by altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more accurate tools for diagnostic purposes.

2019-08-30 | GSE132236 | GEO

Elucidating the etiology and molecular pathogenicity of infectious diarrhea by high throughput RNA sequencing

Project description:Diarrhea remains a major cause of death in children. Current diagnostic methods largely rely on stool culture and suffer from low sensitivity and inadequate specificity, often leading to inappropriate treatment. The objective of the present study was to use RNA sequencing (RNAseq) analysis to determine blood transcriptional profiles specific for several common pathogenic bacteria and viruses that cause diarrhea in children. We collected whole blood samples from children in Mexico having diarrhea associated with a single pathogen and without systemic complications. Our RNAseq data suggested that the blood signatures can differentiate children with diarrhea from healthy children either with or without bacterial colonization. Moreover, we detected different expression profiles from bacterial and viral infection, demonstrating for the first time the use of RNAseq to identify the etiology of infectious diarrhea.

2015-06-04 | GSE69529 | GEO

Evaluating in vitro culture medium of mouse gut microbiome

Project description:The mice stool samples were collected for culturing with different medium for understanding the role of different medium component on the microbiome.

2018-06-15 | PXD006808 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data